From: Benjamin Auder <benjamin.auder@somewhere>
Date: Thu, 23 Feb 2017 18:49:45 +0000 (+0100)
Subject: merge selectVariables.R doc and selectiontotale.R code into selectVariables.R
X-Git-Url: https://git.auder.net/%7B%7B%20asset%28%27mixstore/css/user/current/git-logo.png?a=commitdiff_plain;h=7064275b23125c87a30fbdbd690eeb4d8c557420;p=valse.git

merge selectVariables.R doc and selectiontotale.R code into selectVariables.R
---

diff --git a/R/selectVariables.R b/R/selectVariables.R
index 3f58ea3..92baec8 100644
--- a/R/selectVariables.R
+++ b/R/selectVariables.R
@@ -1,6 +1,5 @@
-#' selectVaribles
-#' It is a function which construct, for a given lambda, the sets of
-#' relevant variables and irrelevant variables.
+#' selectVariables
+#' It is a function which construct, for a given lambda, the sets of relevant variables.
 #'
 #' @param phiInit an initial estimator for phi (size: p*m*k)
 #' @param rhoInit an initial estimator for rho (size: m*m*k)
@@ -15,76 +14,32 @@
 #' @param thres	 threshold to consider a coefficient to be equal to 0
 #' @param tau		 threshold to say that EM algorithm has converged
 #'
-#' @return TODO
+#' @return a list of outputs, for each lambda in grid: selected,Rho,Pi
 #'
 #' @examples TODO
 #'
 #' @export
-selectVariables <- function(phiInit,rhoInit,piInit,gamInit,
-	mini,maxi,gamma,glambda,X,Y,thres,tau)
+selectVariables = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda,X,Y,seuil,tau)
 {
-	dimphi <- dim(phiInit)
-	p <- dimPhi[1]
-	m <- dimPhi[2]
-	k <- dimPhi[3]
-	L <- length(glambda);
-	A1 <- array(0, dim <- c(p,m+1,L))
-	A2 <- array(0, dim <- c(p,m+1,L))
-	Rho <- array(0, dim <- c(m,m,k,L))
-	Pi <- array(0, dim <- c(k,L));
-
-	# For every lambda in gridLambda, comutation of the coefficients
-	for (lambdaIndex in c(1:L))
+	cl = parallel::makeCluster( parallel::detectCores() / 4 )
+	parallel::clusterExport(cl=cl,
+		varlist=c("phiInit","rhoInit","gamInit","mini","maxi","glambda","X","Y","seuil","tau"),
+		envir=environment())
+	#Pour chaque lambda de la grille, on calcule les coefficients
+	out = parLapply( 1:L, function(lambdaindex)
 	{
-		Res <- EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,
-			gamma,glambda[lambdaIndex],X,Y,tau);
-		phi <- Res$phi
-		rho <- Res$rho
-		pi <- Res$pi
-
-		# If a coefficient is larger than the threshold, we keep it
-		selectedVariables <- array(0, dim = c(p,m))
-		discardedVariables <- array(0, dim = c(p,m))
-		atLeastOneSelectedVariable <- false
-		for (j in c(1:p))
-		{
-			cpt <- 1
-			cpt2 <-1
-			for (mm in c(1:m))
-			{
-				if (max(abs(phi[j,mm,])) > thres)
-				{
-					selectedVariables[j,cpt] <- mm
-					cpt <- cpt+1
-					atLeastOneSelectedVariable <- true
-				} else
-				{
-					discardedVariables[j,cpt2] <- mm
-					cpt2 <- cpt2+1
-				}
-			}
-		}
+		params = EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda[lambdaIndex],X,Y,tau)
 
-		# If no coefficients have been selected, we provide the zero matrix
-		# We delete zero coefficients: vec = indices of zero values
-		if (atLeastOneSelectedVariable)
-		{
-			vec <- c()
-			for (j in c(1:p))
-			{
-				if (selectedVariables(j,1) != 0)
-					vec <- c(vec,j)
-				# Else ( NOTE: [auder] else ?! TODO: explain? )
-				# we provide the indices of relevant coefficients
-				A1[,1,lambdaIndex] <- c(vec,rep(0,p-length(vec)))
-				A1[1:length(vec),2:(m+1),lambdaIndex] <- selectedVariables[vec,]
-				A2[,1,lambdaIndex] <- 1:p
-				A2[,2:(m+1),lambdaIndex] <- discardedVariables
-				Rho[,,,lambdaIndex] <- rho
-				Pi[,lambdaIndex] <- pi
-			}
-		}
-	}
+		p = dim(phiInit)[1]
+		m = dim(phiInit)[2]
+		#selectedVariables: list where element j contains vector of selected variables in [1,m]
+		selectedVariables = lapply(1:p, function(j) {
+			#from boolean matrix mxk of selected variables obtain the corresponding boolean m-vector,
+			#and finally return the corresponding indices
+			seq_len(m)[ apply( abs(params$phi[j,,]) > seuil, 1, any ) ]
+		})
 
-	return(res = list(A1 = A1, A2 = A2 , Rho = Rho, Pi = Pi))
+		list("selected"=selectedVariables,"Rho"=params$Rho,"Pi"=params$Pi)
+	})
+	parallel::stopCluster(cl)
 }
diff --git a/R/selectiontotale.R b/R/selectiontotale.R
deleted file mode 100644
index 673bc3b..0000000
--- a/R/selectiontotale.R
+++ /dev/null
@@ -1,25 +0,0 @@
-#Return a list of outputs, for each lambda in grid: selected,Rho,Pi
-selectiontotale = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda,X,Y,seuil,tau)
-{
-	cl = parallel::makeCluster( parallel::detectCores() / 4 )
-	parallel::clusterExport(cl=cl,
-		varlist=c("phiInit","rhoInit","gamInit","mini","maxi","glambda","X","Y","seuil","tau"),
-		envir=environment())
-	#Pour chaque lambda de la grille, on calcule les coefficients
-	out = parLapply( 1:L, function(lambdaindex)
-	{
-		params = EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda[lambdaIndex],X,Y,tau)
-
-		p = dim(phiInit)[1]
-		m = dim(phiInit)[2]
-		#selectedVariables: list where element j contains vector of selected variables in [1,m]
-		selectedVariables = lapply(1:p, function(j) {
-			#from boolean matrix mxk of selected variables obtain the corresponding boolean m-vector,
-			#and finally return the corresponding indices
-			seq_len(m)[ apply( abs(params$phi[j,,]) > seuil, 1, any ) ]
-		})
-
-		list("selected"=selectedVariables,"Rho"=params$Rho,"Pi"=params$Pi)
-	})
-	parallel::stopCluster(cl)
-}